Our Research

Methyl TROSY and 15N,13C-direct-detection experiments allow molecular species as large as 1 MDa to be interrogated by solution NMR. In this remit, NMR has unique capabilities to study:

1. Transient interactions, which lie at the heart of several important enzymatic processes;
2. Complexes involving dynamical regions, subject to regulation through the environment and binding partners;
3. Complexes existing in multiple conformations

References

Teresa Carlomagno and colleagues

• Graziadei, F. Gabel, J. Kirkpatrick, T. Carlomagno (2020). The guide sRNA sequence determines the activity level of Box C/D RNPs. eLife 9:e50027 doi: 10.7554/eLife.50027
• N. Danilenko, L. Lercher, F. Gabel, J. Kirkpatrick, T. Carlomagno (2019). Histone chaperone exploits intrinsic disorder to switch acetylation specificity. Nature Communications 10, Article number: 3435
• E. Karaca, J.P.G.L.M. Rodrigues, A. Graziadei, A.M.J.J. Bonvin, T. Carlomagno (2017). An Integrative framework for structure determination of molecular machines. Nature Methods 14, 897–902
• T.C.R. Miller, B. Simon, V. Rybin, H. Grötsch, T. Carlomagno*, C. W. Müller (2016). A bromodomain-DNA interaction facilitates acetylation-dependent bivalent nucleosome recognition by the BET protein Brdt. Nature Communications doi: 10.1038/NCOMMS13855
• Lapinaite, B. Simon, L. Skjaerven, M. Rakwalska-Bange, F.Gabel, T. Carlomagno (2013). The structure of the Box C/D enzyme reveals regulation of rRNA methylation. Nature 502, 519-523

The paradigm of the (folded) structure–function relationship has been challenged by a revolutionary paper (Borgia et al. Nature 2018) describing a functional complex between two intrinsically unfolded proteins, which both remain disordered upon interaction.

Because of their abundance in the eukaryotic proteome, disordered protein motifs will indisputably be protagonists in structural biology, and NMR is the only technique able to characterize them at atomic-resolution.

New methods must be developed to go beyond the conventional structure determination process, as the concept of single, well-defined structures is replaced by a large but biased ensemble of transient conformations.

References

Teresa Carlomagno and colleagues

• N. Danilenko, L. Lercher, F. Gabel, J. Kirkpatrick, T. Carlomagno (2019). Histone chaperone exploits intrinsic disorder to switch acetylation specificity. Nature Communications 10, Article number: 3435

RNA biology has gained immense importance in the past 3 decades, following the discovery of the pivotal regulatory role of RNA in cellular processes, including those related to diseases (e.g. infection, cancer, neuropathologies).

Structural biology of RNA is challenging due to the conformational plasticity of the RNA. Solid-state NMR is unique in that it guarantees access to atomic resolution structural information with no inherent limitation of molecular weight; consequently, it can adopt an irreplaceable role in RNA structural biology.

The facility offers world-wide unique expertise in ssNMR applied to RNA, as well as in RNA structure and dynamics by solution NMR.

References

Teresa Carlomagno and colleagues

• P.I. Aguion, J. Kirkpatrick, T. Carlomagno, A. Marchanka (2021). Identification of RNA base pairs and complete assignment of nucleobase resonances by proton-detected solid-state NMR spectroscopy at 100 kHz MAS. Angewandte Chemie 60, 23903-23910
• M. Ahmed, A. Marchanka, T. Carlomagno (2020). Structure of a protein-RNA complex by ssNMR. Angewandte Chemie 59, 6866-6873 doi: 10.1002/anie.201915465
• Marchanka, J. Stanek, G. Pintacuda, T. Carlomagno (2018). Rapid access to RNA resonances by proton-detected solid-state NMR at >100 kHz MAS. Chemical Communications 54, 8972 – 8975
• Marchanka, B. Simon, G. Althoff-Ospelt, T. Carlomagno (2015). RNA structure determination by solid-state NMR spectroscopy. Nature Communications, doi: 10.1038/ncomms8024
• S. Asami, M. Rakwalska-Bange, T. Carlomagno, B. Reif (2013). Protein/RNA interfaces probed by 1 H detected MAS solid-state NMR spectroscopy. Angewandte Chemie 52, 2345-2349
• Marchanka, B. Simon, T. Carlomagno (2013). A suite of solid-state NMR experiments for RNA intranucleotide resonance assignment in a 21 kDa protein-RNA complex. Angewandte Chemie 52, 9996-10001

Besides solving new biomolecular structures, NMR is used to reveal the molecular motions that underline function. For example, NMR has revealed that the access to multiple conformational states is critical for enzymatic function and the kinetics of transitions between these states determines the regulation of enzymatic activities.

For regulatory protein domains, NMR-derived insights into allosteric effects and conformational dynamics have achieved a better understanding of protein–ligand interactions in drug-discovery.

NMR is even sensitive to the presence of highly transient states and can reveal important insights into their structure that are not accessible by any other method.

Our structural biology users are funded by the BBSRC, Cancer Research UK, EU, MRC, Wellcome Trust and other funding agencies

The classical process of discovery and development of small-molecule drugs benefits from NMR-based fragment screening and structural validation of binding modes.

More importantly, and unique to NMR, is its capacity to provide insights into allosteric effects and conformational dynamics, which greatly enhance the likelihood of success of structure-based drug-discovery campaigns.

Our facility promotes the application of NMR in drug-discovery by offering and developing state-of-the-art technologies together with our users.

References

Teresa Carlomagno and colleagues

• L. Skjærven, L. Codutti, A. Angelini, M. Grimaldi, D. Latek, P. Monecke, M. Dreyer, T. Carlomagno (2013). Protein-ligand induced-fit docking with NMR guided rescoring. Journal of the American Chemical Society 135, 5819-5827
• J. Orts, S. Bartoschek, C. Griesinger, P. Monecke, T. Carlomagno (2012). An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude. Journal of Biomolecular NMR 52, 23-30
• J. Orts, C. Griesinger, T. Carlomagno (2009). The INPHARMA technique for pharmacophore mapping: A theoretical guide to the method. Journal of Magnetic Resonance 200, 64-73
• J. Orts, J. Tuma, M. Reese, S.K. Grimm, P. Monecke, S. Bartoscheck, A. Schiffer, K.U. Wendt, C. Griesinger, T. Carlomagno (2008). Crystallography independent determination of ligand binding modes. Angewandte Chemie 47, 7736-7740
• V.M. Sanchez-Pedregal, M. Reese, J. Meiler, M.J.J. Blommers, C. Griesinger, T. Carlomagno (2005). The INPHARMA method: Protein mediated Interligand NOEs for Pharmacophore Mapping. Angewandte Chemie 44, 4172-4175

Metabolomics refers to the study of the dynamic concentrations of small biological molecules produced by living cells. It  is used in pharmacology and toxicology research.

Metabolomics relies on NMR to monitor fluctuations in the levels of many metabolites simultaneously, which provides valuable information about cellular responses to toxic or therapeutic agents.

The advantages of NMR are its high analytical reproducibility, simple sample preparation and non-destructive analysis. The Phenome Centre Birmingham offers comprehensive collaborative services on clinical and biological metabolomics projects (see also the Metabolomics Initiative). Alongside classical metabolomics, the facility also supports metabolic tracing, which is the method of choice when a more directed analysis of the activity of specific metabolic pathways is required.

In metabolic tracing, NMR is used to follow the fate of specifically isotopically labelled metabolites (see also the Metabolic Tracer Analysis Core, MTAC).

Local developments include:

• New, free and open source NMR data processing software, MetaboLabPy, developed and actively supported by Christian Ludwig, the standard NMR processing software chosen by the Phenome Centre Birmingham.
• New methodology from Christian Ludwig for integration of NMR and MS data for metabolite tracing (CANMS) using a single sample.
• Christian Ludwig and colleagues have developed techniques for the rapid collection of NMR data, in a quantitative manner, suitable for tracer-based metabolism studies (HS-TrAM).
• The Phenome Centre Birmingham was established by Mark Viant and colleagues to offer comprehensive collaborative services (including NMR and MS data analysis) for clinical and biological projects.
• Mark Viant and colleagues have jointly developed protocols for the preparation and extraction of cancer cell lines, plasma samples and tissues.